I believe that a MR gemstone would be more rare than a HF version. We haven't seen many MR gemstone cards yet.
I calculated the odds of pulling a MR gemstone refractor at around 1:56 per pack. Based on there being 3718 out of 1.02m total cards. The odds of a MR HF are the true 1:124.
if there are 3718 MR refractors out of a million cards I think the odds would be 1:268. But on a side note there are 11 potential MR refractors but only 5 have been discovered. To date no refractors or holofoils have been found for MR3, MR4A, MR6, MR6A, MR7A, and MR8. So either these cards were dispersed into later boxes or weren't made at all. If only 5 MR refractors exist odds would be more like 1:645 I believe